Repo2docker: Investigate using / supporting renv with R
Proposed change
https://rstudio.github.io/renv/ seems to be a new way to do isolated package dependencies in R from the wonderful folks at RStudio. We should investigate it to see if there's any use repo2docker can get out of that.
Alternative options
The current similar alternative is packrat, which is a lot more heavyweight and not particularly popularly used (from what I'm told).
Who would use this feature?
R folks who want isolated environments, like virtualenvs. I am not entirely sure how that fits into repo2docker, since we already use containers.
yuvipanda
All 9 comments
One way to use this is to support/detect the presence of a renv.lock and use that to install packages instead of install.R (or as a small step towards phasing out that file).
From reading their website for a bit: it would be interesting to know why they don't have a renv where you can write down what packages you want and them from that generate the lockfile renv.lock.
betatim
on 2 May 2019
I like it. /cc @karthik @cboettig
yuvipanda
on 2 May 2019
Looks pretty good to me.
Curious what you think of https://rstudio.github.io/renv/articles/python.html?
cboettig
on 2 May 2019
From reading their website for a bit: it would be interesting to know why they don't have a renv where you can write down what packages you want and them from that generate the lockfile renv.lock.
I believe renv is following packrat method of detecting all dependencies based on finding library() calls in the code (and then computing the recursive dependencies); probably based on the reasonable assumption that going by actual library() calls found in the user's code will be more accurate than assuming users actually remember to add each package manually to some new config file. (Looks like it will similarly generate a requirements.txt from R code that requires python packages :-) ).
cboettig
on 2 May 2019
I approve using renv. Happy to contribute some effort here.
karthik
on 2 May 2019
What do people think of making a new build pack (that inherits from the R build pack) that detects the renv.lock, installs the renv package, and then runs renv::restore().
We already support requirements.txt so we should make sure to set renv (and reticulate?) to use the conda env that would be created if a requirements.txt is found in the repository.
betatim
on 3 May 2019
I like it, @betatim. I think renv.lock should take precedence over install.R, so maybe renv.locks' buildpack should be inherited by the current one? Doesn't matter too much though.
yuvipanda
on 3 May 2019
I think of precedence being defined by the order that build packs are searched and inheritance for composing the different (compatible) environments. In my mind we'd reuse some of the infrastructure from the existing R build pack (how does the R binary get installed, RStudio, etc) but the packages that get installed come from renv.lock instead of install.R.
betatim
on 3 May 2019
Just keep in mind: if composable build packs get re-introduced, then the "should take precedence" must be realised somehow.
nuest
on 17 Sep 2019
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Most helpful comment
I believe
renvis followingpackratmethod of detecting all dependencies based on findinglibrary()calls in the code (and then computing the recursive dependencies); probably based on the reasonable assumption that going by actuallibrary()calls found in the user's code will be more accurate than assuming users actually remember to add each package manually to some new config file. (Looks like it will similarly generate arequirements.txtfrom R code that requires python packages :-) ).